Ecnomidae are a family of seven previously accepted extant genera having a typical Gondwanan distribution, except one genus (Ecnomus) being widely distributed also in the Oriental and Palearctic regions. We analysed a molecular data set of 3379 characters representing the sum of four different protein-coding genes (COI, CAD, EF-1a and POL-II). Six equally most parsimonious trees were generated from the combined data set, distributed into two distinct islands. In all maximum parsimony (MP) trees the Ecnomidae is monophyletic when the genus Zelandoptila (Psychomyiidae) is included. The sister group to Ecnomidae including Zelandoptila is Pseudoneureclipsis, previously classified in the other families. This sister-group relationship contradicts earlier findings that the Polycentropodidae are the sister group to Ecnomidae. A Bayesian analysis resulted in a monophyletic Ecnomidae when accepting inclusion of Pseudoneureclipsis, which contradicts the results from the MP analysis by leaving Zelandoptila as the sister group to Ecnomidae including Pseudoneureclipsis. In the majority rule tree from this analysis Polycentropodidae form the sister group to Ecnomidae. We were not able to obtain a monophyletic Ecnomus due to the inclusion of Psychomyillodes. We conclude that the genus Zelandoptila or Pseudoneureclipsis probably belongs to the Ecnomidae, and that Psychomyiellodes and Ecnomus are synonyms. Three additional, as yet undescribed monotypic genera from Australia and New Caledonia remain to be erected in Ecnomidae. © The Willi Hennig Society 2009.